Sounds like you might have a pinched ground wire. By design, the 12V+ is supplied to all 3 coils constant when the key is turned on. Then the ground lead runs from each coil to the ignition controller and is switched on/off based off the hall sensor inputs.
If you unplug the controller, measure the ground wire of each coil, it should be an "open" circuit. If not, you need to locate the fault.
Coil #1 switched ground lead should be Black/Blue, the 12+ lead should be Green/Yellow